[gmx-users] Help: Gromacs Installation

[Roland Schulz]

This seems to be a problem with your MPI library. Test to see whether other
MPI programs don't have the same problem. If it is not GROMACS specific
please ask on the mailinglist of your MPI library. If it only happens with
GROMACS be more specific about what your setup is (what MPI library, what
hardware, ...).

Also you could use the latest GROMACS 4.5.x. It has built in thread support
and doesn't need MPI as long as you only run on n cores within one SMP node.

Roland

On Wed, Apr 27, 2011 at 2:13 PM, Hrachya Astsatryan <hrach at sci.am> wrote:

> Dear Mark Abraham & all,
>
> We  used another benchmarking systems, such as d.dppc on 4 processors, but
> we have the same problem (1 proc use about 100%, the others 0%).
> After for a while we receive the following error:
>
> Working directory is /localuser/armen/d.dppc
> Running on host wn1.ysu-cluster.grid.am
> Time is Fri Apr 22 13:55:47 AMST 2011
> Directory is /localuser/armen/d.dppc
> ____START____
> Start: Fri Apr 22 13:55:47 AMST 2011
> p2_487:  p4_error: Timeout in establishing connection to remote process: 0
> rm_l_2_500: (301.160156) net_send: could not write to fd=5, errno = 32
> p2_487: (301.160156) net_send: could not write to fd=5, errno = 32
> p0_32738:  p4_error: net_recv read:  probable EOF on socket: 1
> p3_490: (301.160156) net_send: could not write to fd=6, errno = 104
> p3_490:  p4_error: net_send write: -1
> p3_490: (305.167969) net_send: could not write to fd=5, errno = 32
> p0_32738: (305.371094) net_send: could not write to fd=4, errno = 32
> p1_483:  p4_error: net_recv read:  probable EOF on socket: 1
> rm_l_1_499: (305.167969) net_send: could not write to fd=5, errno = 32
> p1_483: (311.171875) net_send: could not write to fd=5, errno = 32
> Fri Apr 22 14:00:59 AMST 2011
> End: Fri Apr 22 14:00:59 AMST 2011
> ____END____
>
> We tried new version of Gromacs, but receive the same error.
> Please, help us to overcome the problem.
>
>
> With regards,
> Hrach
>
>
> On 4/22/11 1:41 PM, Mark Abraham wrote:
>
>> On 4/22/2011 5:40 PM, Hrachya Astsatryan wrote:
>>
>>> Dear all,
>>>
>>> I would like to inform you that I have installed the gromacs4.0.7 package
>>> on the cluster (nodes of the cluster are 8 core Intel, OS: RHEL4 Scientific
>>> Linux) with the following steps:
>>>
>>> yum install fftw3 fftw3-devel
>>> ./configure --prefix=/localuser/armen/gromacs --enable-mpi
>>>
>>> Also I have downloaded gmxbench-3.0 package and try to run d.villin to
>>> test it.
>>>
>>> Unfortunately it wok fine until np is 1,2,3, if I use more than 3 procs I
>>> receive low CPU balancing and the process in hanging.
>>>
>>> Could you, please, help me to overcome the problem?
>>>
>>
>> Probably you have only four physical cores (hyperthreading is not normally
>> useful), or your MPI is configured to use only four cores, or these
>> benchmarks are too small to scale usefully.
>>
>> Choosing to do a new installation of a GROMACS version that is several
>> years old is normally less productive than the latest version.
>>
>> Mark
>>
>>
>>
>>
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